Broad non-coding transcription suggests genome surveillance by RNA Polymerase V

Eukaryotic genomes are pervasively transcribed, yet most transcribed sequences lack conservation or known biological functions. In Arabidopsis thaliana RNA polymerase V (Pol V) produces non-coding transcripts, which base-pair with small interfering RNA (siRNA) and allow specific establishment of RNA-directed DNA methylation (RdDM) on transposable elements. Here, we show that Pol V transcribes much more broadly than previously expected, including subsets of both heterochromatic and euchromatic regions. At already established RdDM targets Pol V and siRNA work together to maintain silencing. In contrast, some euchromatic sequences do not give rise to siRNA but are covered by low levels of Pol V transcription, which is needed to establish RdDM de novo if a transposon is reactivated. We propose a model where Pol V surveils the genome to make it competent to silence newly activated or integrated transposons. This indicates that pervasive transcription of non-conserved sequences may serve an essential role in maintenance of genome integrity. Overall design: Immunoprecipitation followed by Analysis of RNA Ends (IPARE) with an anti-NRPE1 antibody was performed on 24 samples, which include 11 different genotypes (Col-0:6replicates; nrpe1:5replicates; spt5l,ago4,dms5-1,drd3-3: 2replicates each, drd1,dms3,suvh2, suvh9, suvh2/suvh9: 1replicate each)